File preparation

File preparation by ANNOVAR

  • Command used in ANNOVAR:

convert2annovar.pl -format rsid T1D.txt -dbsnpfile humandb/hg19_snp138.txt > T1D_MS_formatted

  • 119 SNPs records input; 110 SNPs records as output, 9 SNPs missing
##     V1       V2       V3 V4 V5        V6
## 1 chr6 29692305 29692305  A  G rs1632953
## 2 chr6 29694427 29694427  C  T rs1059174
## 3 chr6 29696209 29696209  G  A rs1736921
## 4 chr6 29704083 29704083  C  T rs1736916
## 5 chr6 29704400 29704400  T  C rs1736913
## 6 chr6 29708222 29708222  T  C rs1610603
  • Identify 9 missing SNPs
## [1] "rs6931717"  "rs7452756"  "rs12199773" "rs6937967"  "rs12178292"
## [6] "rs10456058" "rs7382662"  "rs10807118" "rs10947377"

  • missing SNP IDs were renamed from PUBMED

    rs6931717 > rs3095345

rs7452756 > rs4516988

rs12199773 > rs3130952

rs6937967 >  rs3130534

rs12178292 > rs2844558

rs10456058 >  rs2734573

rs7382662 >  rs3129305

rs10807118 >  rs3130578

rs10947377 > rs3130179

  • Created a new file T1D_2.txt after chainging SNP ids

  • Rerun in ANNOVAR and obtained results for all 119 SNPs

##     V1       V2       V3 V4 V5        V6
## 1 chr6 29692305 29692305  A  G rs1632953
## 2 chr6 29694427 29694427  C  T rs1059174
## 3 chr6 29696209 29696209  G  A rs1736921
## 4 chr6 29704083 29704083  C  T rs1736916
## 5 chr6 29704400 29704400  T  C rs1736913
## 6 chr6 29708222 29708222  T  C rs1610603

ANNOVAR ANALYSIS

Gene based annotation

Known Gene (UCSC)

##   Genomic region      Gene Chromosome     BP_1     BP_2 A1 A2       SNP
## 1       intronic     HLA-F       chr6 29692305 29692305  A  G rs1632953
## 2   ncRNA_exonic HLA-F-AS1       chr6 29694427 29694427  C  T rs1059174
## 3   ncRNA_exonic HLA-F-AS1       chr6 29696209 29696209  G  A rs1736921
## 4   ncRNA_exonic HLA-F-AS1       chr6 29704083 29704083  C  T rs1736916
## 5   ncRNA_exonic HLA-F-AS1       chr6 29704400 29704400  T  C rs1736913
## 6 ncRNA_intronic HLA-F-AS1       chr6 29708222 29708222  T  C rs1610603

Ensembel Gene

##   Genomic region            Gene Chromosome     BP_1     BP_2 A1 A2       SNP
## 1       intronic ENSG00000204642       chr6 29692305 29692305  A  G rs1632953
## 2   ncRNA_exonic ENSG00000214922       chr6 29694427 29694427  C  T rs1059174
## 3   ncRNA_exonic ENSG00000214922       chr6 29696209 29696209  G  A rs1736921
## 4   ncRNA_exonic ENSG00000214922       chr6 29704083 29704083  C  T rs1736916
## 5   ncRNA_exonic ENSG00000214922       chr6 29704400 29704400  T  C rs1736913
## 6 ncRNA_intronic ENSG00000214922       chr6 29708222 29708222  T  C rs1610603

Ref Gene (NCBI)

##   Genomic_region      Gene Chromosome     BP_1     BP_2 A1 A2       SNP
## 1       intronic     HLA-F       chr6 29692305 29692305  A  G rs1632953
## 2   ncRNA_exonic HLA-F-AS1       chr6 29694427 29694427  C  T rs1059174
## 3   ncRNA_exonic HLA-F-AS1       chr6 29696209 29696209  G  A rs1736921
## 4 ncRNA_intronic HLA-F-AS1       chr6 29704083 29704083  C  T rs1736916
## 5 ncRNA_intronic HLA-F-AS1       chr6 29704400 29704400  T  C rs1736913
## 6 ncRNA_intronic HLA-F-AS1       chr6 29708222 29708222  T  C rs1610603
  • We will use known gene as reference to create table